Index

Symbols

--add-ga4gh-tool-registry cwltool command line option --basedir cwltool command line option --beta-conda-dependencies cwltool command line option --beta-dependencies-directory cwltool command line option --beta-dependency-resolvers-configuration cwltool command line option --beta-use-biocontainers cwltool command line option --cachedir cwltool command line option --cidfile-dir cwltool command line option --cidfile-prefix cwltool command line option --compute-checksum cwltool command line option --copy-outputs cwltool command line option --custom-net cwltool command line option --debug cwltool command line option --default-container cwltool command line option --disable-color cwltool command line option --disable-ga4gh-tool-registry cwltool command line option --disable-js-validation cwltool command line option --disable-pull cwltool command line option --doc-cache cwltool command line option --enable-color cwltool command line option --enable-dev cwltool command line option --enable-ext cwltool command line option --enable-ga4gh-tool-registry cwltool command line option --enable-pull cwltool command line option --eval-timeout cwltool command line option --force-docker-pull cwltool command line option --help cwltool command line option --js-console cwltool command line option --js-hint-options-file cwltool command line option --leave-container cwltool command line option --leave-outputs cwltool command line option --leave-tmpdir cwltool command line option --log-dir cwltool command line option --make-template cwltool command line option --move-outputs cwltool command line option --mpi-config-file cwltool command line option --no-compute-checksum cwltool command line option --no-container cwltool command line option --no-doc-cache cwltool command line option --no-match-user cwltool command line option --no-read-only cwltool command line option --no-warnings cwltool command line option --non-strict cwltool command line option --on-error cwltool command line option

--outdir cwltool command line option --overrides cwltool command line option --pack cwltool command line option --parallel cwltool command line option --parallel-max cwltool command line option --podman cwltool command line option --preserve-entire-environment cwltool command line option --preserve-environment cwltool command line option --print-deps cwltool command line option --print-dot cwltool command line option --print-input-deps cwltool command line option --print-pre cwltool command line option --print-rdf cwltool command line option --print-subgraph cwltool command line option --print-supported-versions cwltool command line option --print-targets cwltool command line option --quiet cwltool command line option --rdf-serializer cwltool command line option --relative-deps cwltool command line option --relax-path-checks cwltool command line option --rm-container cwltool command line option --rm-tmpdir cwltool command line option --single-process cwltool command line option --single-step cwltool command line option --singularity cwltool command line option --singularity-sandbox-path cwltool command line option --skip-schemas cwltool command line option --strict cwltool command line option --strict-cpu-limit cwltool command line option --strict-memory-limit cwltool command line option --target cwltool command line option --timestamps cwltool command line option --tmp-outdir-prefix cwltool command line option --tmpdir-prefix cwltool command line option --tool-help cwltool command line option --udocker cwltool command line option --user-space-docker-cmd cwltool command line option --validate cwltool command line option --verbose cwltool command line option --version cwltool command line option --write-summary cwltool command line option -h cwltool command line option -t cwltool command line option -w cwltool command line option

_

__author__ (in module cwltool) __call__() (cwltool.argparser.AppendAction method) (cwltool.argparser.FSAction method) (cwltool.argparser.FSAppendAction method) (cwltool.executors.JobExecutor method) (cwltool.factory.Callable method) __citation__ (in module cwltool.cwlprov.provenance_constants)

__contains__() (cwltool.pathmapper.PathMapper method) __iter__() (cwltool.pathmapper.PathMapper method) __repr__() (cwltool.job.JobBase method) __str__() (cwltool.command_line_tool.ParameterOutputWorkflowException method) (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) (cwltool.cwlprov.ro.ResearchObject method) (cwltool.factory.WorkflowStatus method) (cwltool.process.Process method)

A

abspath() (in module cwltool.stdfsaccess) AbstractOperation (class in cwltool.command_line_tool) ACCOUNT_UUID (in module cwltool.cwlprov.provenance_constants) activity_has_provenance() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) add() (cwltool.secrets.SecretStore method) (cwltool.task_queue.TaskQueue method) add_annotation() (cwltool.cwlprov.ro.ResearchObject method) add_argument() (in module cwltool.argparser) add_data_file() (cwltool.cwlprov.ro.ResearchObject method) add_file_or_directory_volume() (cwltool.docker.DockerCommandLineJob method) (cwltool.job.ContainerCommandLineJob method) (cwltool.singularity.SingularityCommandLineJob method) add_sizes() (in module cwltool.process) add_tagfile() (cwltool.cwlprov.ro.ResearchObject method) add_to_manifest (cwltool.cwlprov.provenance_profile.ProvenanceProfile attribute) add_to_manifest() (cwltool.cwlprov.ro.ResearchObject method) add_uri() (cwltool.cwlprov.ro.ResearchObject method) add_volumes() (cwltool.job.ContainerCommandLineJob method) add_writable_directory_volume() (cwltool.docker.DockerCommandLineJob method) (cwltool.job.ContainerCommandLineJob method) (cwltool.singularity.SingularityCommandLineJob method) add_writable_file_volume() (cwltool.docker.DockerCommandLineJob method) (cwltool.job.ContainerCommandLineJob method) (cwltool.singularity.SingularityCommandLineJob method)

adjustDirObjs() (in module cwltool.utils) adjustFileObjs() (in module cwltool.utils) Aggregate (class in cwltool.cwlprov) allocated_cores (cwltool.executors.MultithreadedJobExecutor attribute) allocated_cuda (cwltool.executors.MultithreadedJobExecutor attribute) allocated_ram (cwltool.executors.MultithreadedJobExecutor attribute) ALLUPDATES (in module cwltool.update) Annotation (in module cwltool.cwlprov) annotations (cwltool.cwlprov.ro.ResearchObject attribute) append_volume() (cwltool.docker.DockerCommandLineJob static method) (cwltool.job.ContainerCommandLineJob static method) (cwltool.singularity.SingularityCommandLineJob static method) (cwltool.udocker.UDockerCommandLineJob static method) append_word_to_default_user_agent() (in module cwltool.main) AppendAction (class in cwltool.argparser) arg_parser() (in module cwltool.argparser) ArgumentException aslist() (in module cwltool.utils) AuthoredBy (class in cwltool.cwlprov) avroize_type() (in module cwltool.process) avsc_names (cwltool.context.LoadingContext attribute)

B

bagged_size (cwltool.cwlprov.ro.ResearchObject attribute) base_uri (cwltool.argparser.FSAction attribute) (cwltool.argparser.FSAppendAction attribute) (cwltool.cwlprov.ro.ResearchObject attribute) basedir (cwltool.context.RuntimeContext attribute) (cwltool.stdfsaccess.StdFsAccess attribute) bind_input() (cwltool.builder.Builder method) bindings (cwltool.builder.Builder attribute) boot2docker_id() (in module cwltool.docker_id)

boot2docker_running() (in module cwltool.docker_id) build_job_script() (cwltool.builder.Builder method) (cwltool.software_requirements.DependenciesConfiguration method) Builder (class in cwltool.builder) builder (cwltool.command_line_tool.ExpressionJob attribute) (cwltool.context.RuntimeContext attribute) (cwltool.job.JobBase attribute) bundledAs (cwltool.cwlprov.Aggregate attribute) bytes2str_in_dicts() (in module cwltool.utils)

C

cachebuilder (cwltool.command_line_tool.CallbackJob attribute) cachedir (cwltool.context.RuntimeContext attribute) Callable (class in cwltool.factory) CallbackJob (class in cwltool.command_line_tool) can_assign_src_to_sink() (in module cwltool.checker) check_adjust() (in module cwltool.command_line_tool) check_output_and_strip() (in module cwltool.docker_id) check_types() (in module cwltool.checker) check_valid_locations() (in module cwltool.command_line_tool) check_working_directories() (in module cwltool.main) checkRequirements() (cwltool.process.Process method) checksum_copy() (in module cwltool.cwlprov) checkversion() (in module cwltool.update) choose_process() (in module cwltool.main) choose_step() (in module cwltool.main) choose_target() (in module cwltool.main) cidfile_dir (cwltool.context.RuntimeContext attribute) cidfile_prefix (cwltool.context.RuntimeContext attribute) circular_dependency_checker() (in module cwltool.checker) cleanIntermediate() (in module cwltool.process) close() (cwltool.cwlprov.writablebagfile.WritableBagFile method) close_ro() (in module cwltool.cwlprov.writablebagfile) closed (cwltool.cwlprov.ro.ResearchObject attribute) cmd_output_matches() (in module cwltool.docker_id) cmd_output_to_int() (in module cwltool.docker_id) cmp_like_py2() (in module cwltool.utils) codegen_idx (cwltool.context.LoadingContext attribute) collect_output() (cwltool.command_line_tool.CommandLineTool method) collect_output_ports() (cwltool.command_line_tool.CommandLineTool method) collect_outputs (cwltool.job.JobBase attribute) CollectOutputsType (in module cwltool.job) command_line (cwltool.job.JobBase attribute) COMMAND_WITH_DEPENDENCIES_TEMPLATE (in module cwltool.software_requirements) CommandLineJob (class in cwltool.job) CommandLineTool (class in cwltool.command_line_tool) completed (cwltool.workflow_job.ReceiveScatterOutput property) (cwltool.workflow_job.WorkflowJobStep attribute) compute_checksum (cwltool.context.RuntimeContext attribute) compute_checksums() (in module cwltool.process) configure_logging() (in module cwltool.loghandler) conformsTo (cwltool.cwlprov.Aggregate attribute) construct_tool_object (cwltool.context.LoadingContext attribute) container_engine (cwltool.builder.Builder attribute) (cwltool.process.Process attribute) (cwltool.workflow_job.WorkflowJobLoopStep attribute) CONTAINER_TMPDIR (cwltool.job.ContainerCommandLineJob attribute) ContainerCommandLineJob (class in cwltool.job) CONTENT_LIMIT (in module cwltool.utils) content_limit_respected_read() (in module cwltool.builder) content_limit_respected_read_bytes() (in module cwltool.builder) ContextBase (class in cwltool.context) CONTROL_CODE_RE (in module cwltool.job) copy() (cwltool.context.LoadingContext method) (cwltool.context.RuntimeContext method) copy_job_order() (in module cwltool.cwlprov.provenance_profile) copytree_with_merge() (in module cwltool.utils) create_file_and_add_volume() (cwltool.job.ContainerCommandLineJob method) create_job() (in module cwltool.cwlprov.writablebagfile) create_outdir() (cwltool.context.RuntimeContext method) create_runtime() (cwltool.docker.DockerCommandLineJob method) (cwltool.job.ContainerCommandLineJob method) (cwltool.singularity.SingularityCommandLineJob method) create_tmp_dir() (in module cwltool.utils) create_tmpdir() (cwltool.context.RuntimeContext method) createdBy (cwltool.cwlprov.Aggregate attribute) createdOn (cwltool.cwlprov.Aggregate attribute) crossproduct_size() (in module cwltool.workflow_job) cuda_check() (in module cwltool.cuda) cuda_version_and_device_count() (in module cwltool.cuda) custom_net (cwltool.context.RuntimeContext attribute) custom_schemas (in module cwltool.process) CWL_CONTENT_TYPES (in module cwltool) cwl_document cwltool command line option cwl_files (in module cwltool.process) cwl_full_name (cwltool.context.LoadingContext attribute) (cwltool.context.RuntimeContext attribute) CWL_IANA (in module cwltool.process) CWLArtifact (in module cwltool.cwlprov.provenance_profile) CWLPROV (in module cwltool.cwlprov.provenance_constants) CWLPROV_VERSION (in module cwltool.cwlprov.provenance_constants) cwltool module cwltool command line option --add-ga4gh-tool-registry --basedir --beta-conda-dependencies --beta-dependencies-directory --beta-dependency-resolvers-configuration --beta-use-biocontainers --cachedir --cidfile-dir --cidfile-prefix --compute-checksum --copy-outputs --custom-net --debug --default-container --disable-color --disable-ga4gh-tool-registry --disable-js-validation --disable-pull --doc-cache --enable-color --enable-dev --enable-ext --enable-ga4gh-tool-registry --enable-pull --eval-timeout --force-docker-pull --help --js-console --js-hint-options-file --leave-container --leave-outputs --leave-tmpdir --log-dir --make-template --move-outputs --mpi-config-file --no-compute-checksum --no-container --no-doc-cache --no-match-user --no-read-only --no-warnings --non-strict --on-error --outdir --overrides --pack --parallel --parallel-max --podman --preserve-entire-environment --preserve-environment --print-deps --print-dot --print-input-deps --print-pre --print-rdf --print-subgraph --print-supported-versions --print-targets --quiet --rdf-serializer --relative-deps --relax-path-checks --rm-container --rm-tmpdir --single-process --single-step --singularity --singularity-sandbox-path --skip-schemas --strict --strict-cpu-limit --strict-memory-limit --target --timestamps --tmp-outdir-prefix --tmpdir-prefix --tool-help --udocker --user-space-docker-cmd --validate --verbose --version --write-summary -h -t -w cwl_document inputs_object

cwltool.__main__ module cwltool.argparser module cwltool.builder module cwltool.checker module cwltool.command_line_tool module cwltool.context module cwltool.cuda module cwltool.cwlprov module cwltool.cwlprov.provenance_constants module cwltool.cwlprov.provenance_profile module cwltool.cwlprov.ro module cwltool.cwlprov.writablebagfile module cwltool.cwlrdf module cwltool.cwlviewer module cwltool.docker module cwltool.docker_id module cwltool.env_to_stdout module cwltool.errors module cwltool.executors module cwltool.factory module cwltool.flatten module cwltool.job module cwltool.load_tool module cwltool.loghandler module cwltool.main module cwltool.mpi module cwltool.mutation module cwltool.pack module cwltool.pathmapper module cwltool.process module cwltool.procgenerator module cwltool.resolver module cwltool.run_job module cwltool.secrets module cwltool.singularity module cwltool.singularity_utils module cwltool.software_requirements module cwltool.stdfsaccess module cwltool.subgraph module cwltool.task_queue module cwltool.udocker module cwltool.update module cwltool.utils module cwltool.validate_js module cwltool.workflow module cwltool.workflow_job module cwltool_version (cwltool.cwlprov.ro.ResearchObject attribute) cwlVersion (cwltool.builder.Builder attribute) CWLViewer (class in cwltool.cwlviewer)

D

DATA (in module cwltool.cwlprov.provenance_constants) debug (cwltool.builder.Builder attribute) (cwltool.context.LoadingContext attribute) (cwltool.context.RuntimeContext attribute) declare_artefact() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) declare_directory() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) declare_file() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) declare_string() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) dedup() (in module cwltool.utils) default_container (cwltool.context.RuntimeContext attribute) default_loader() (in module cwltool.load_tool) default_make_tool (in module cwltool.context) default_make_tool() (in module cwltool.workflow) default_nproc (cwltool.mpi.MpiConfig attribute) default_stderr (cwltool.context.RuntimeContext attribute) default_stdout (cwltool.context.RuntimeContext attribute) DEFAULT_TMP_PREFIX (in module cwltool.utils) defaultStreamHandler (in module cwltool.loghandler) DependenciesConfiguration (class in cwltool.software_requirements) dependency_resolvers_config_file (cwltool.software_requirements.DependenciesConfiguration attribute) deserialize_env() (in module cwltool.env_to_stdout) dest (cwltool.workflow_job.ReceiveScatterOutput attribute) DestinationsType (in module cwltool.utils) DEVUPDATES (in module cwltool.update) did_callback (cwltool.workflow_job.WorkflowJob attribute) DirectoryAction (class in cwltool.argparser) DirectoryAppendAction (class in cwltool.argparser)

DirentType (class in cwltool.utils) disable_js_validation (cwltool.context.LoadingContext attribute) do_eval() (cwltool.builder.Builder method) do_output_callback() (cwltool.workflow_job.WorkflowJob method) do_update (cwltool.context.LoadingContext attribute) do_validate (cwltool.context.LoadingContext attribute) doc_cache (cwltool.context.LoadingContext attribute) doc_loader (cwltool.process.Process attribute) doc_schema (cwltool.process.Process attribute) docker_exe (in module cwltool.main) docker_exec (cwltool.docker.DockerCommandLineJob attribute) (cwltool.docker.PodmanCommandLineJob attribute) docker_machine_id() (in module cwltool.docker_id) docker_machine_name() (in module cwltool.docker_id) docker_machine_running() (in module cwltool.docker_id) docker_monitor() (cwltool.job.ContainerCommandLineJob method) docker_outdir (cwltool.context.RuntimeContext attribute) docker_stagedir (cwltool.context.RuntimeContext attribute) docker_tmpdir (cwltool.context.RuntimeContext attribute) docker_vm_id() (in module cwltool.docker_id) DockerCommandLineJob (class in cwltool.docker) docloaderctx (in module cwltool.load_tool) document (cwltool.cwlprov.provenance_profile.ProvenanceProfile attribute) dot() (cwltool.cwlviewer.CWLViewer method) dotproduct_scatter() (in module cwltool.workflow_job) DOWN (in module cwltool.subgraph) downloadHttpFile() (in module cwltool.utils) drain() (cwltool.task_queue.TaskQueue method)

E

enable_dev (cwltool.context.LoadingContext attribute) ENCODING (in module cwltool.cwlprov.provenance_constants) engine_uuid (cwltool.cwlprov.provenance_profile.ProvenanceProfile attribute) (cwltool.cwlprov.ro.ResearchObject attribute) ensure_galaxy_lib_available() (in module cwltool.software_requirements) ensure_non_writable() (in module cwltool.utils) ensure_writable() (in module cwltool.utils) entry (cwltool.utils.DirentType attribute) entryname (cwltool.utils.DirentType attribute) env_pass (cwltool.mpi.MpiConfig attribute) env_pass_regex (cwltool.mpi.MpiConfig attribute) env_set (cwltool.mpi.MpiConfig attribute) environment (cwltool.job.JobBase attribute) environment variable CWL_FULL_NAME CWL_SINGULARITY_CACHE CWLTOOL_OPTIONS ORCID XDG_CACHE_HOME XDG_DATA_DIRS XDG_DATA_HOME

error (cwltool.task_queue.TaskQueue attribute) errors (cwltool.validate_js.JSHintJSReturn attribute) eval_resource() (in module cwltool.process) eval_timeout (cwltool.context.LoadingContext attribute) (cwltool.context.RuntimeContext attribute) evalResources() (cwltool.process.Process method) evaluate() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) exceptions (cwltool.executors.MultithreadedJobExecutor attribute) execute() (cwltool.executors.JobExecutor method) (cwltool.executors.NoopJobExecutor method) executor (cwltool.factory.Factory attribute) exists() (cwltool.stdfsaccess.StdFsAccess method) ExpressionJob (class in cwltool.command_line_tool) ExpressionTool (class in cwltool.command_line_tool) extra_flags (cwltool.mpi.MpiConfig attribute) extract_environment() (cwltool.job.JobBase static method)

F

Factory (class in cwltool.factory) factory (cwltool.factory.Callable attribute) fast_parser (cwltool.context.LoadingContext attribute) fast_parser() (in module cwltool.load_tool) fetch_document() (in module cwltool.load_tool) fetcher_constructor (cwltool.context.LoadingContext attribute) FILE_COUNT_WARNING (in module cwltool.process) FileAction (class in cwltool.argparser) FileAppendAction (class in cwltool.argparser) files (cwltool.builder.Builder attribute) files() (cwltool.pathmapper.PathMapper method) fill_in_defaults() (in module cwltool.process) filter() (cwltool.process.LogAsDebugFilter method) (cwltool.validate_js.SuppressLog method) final_output (cwltool.executors.JobExecutor attribute) final_status (cwltool.executors.JobExecutor attribute) finalize_prov_profile() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) find_default_container (cwltool.builder.Builder attribute) (cwltool.context.RuntimeContext attribute) find_default_container() (in module cwltool.main) find_deps() (in module cwltool.main)

find_ids() (in module cwltool.pack) find_run() (in module cwltool.pack) find_step() (in module cwltool.subgraph) flat_crossproduct_scatter() (in module cwltool.workflow_job) flatten() (in module cwltool.flatten) FOAF (in module cwltool.cwlprov.provenance_constants) folder (cwltool.cwlprov.provenance_profile.ProvenanceProfile attribute) (cwltool.cwlprov.ro.ResearchObject attribute) force_docker_pull (cwltool.builder.Builder attribute) (cwltool.context.RuntimeContext attribute) FORCE_SHELLED_POPEN (in module cwltool.job) formatgraph (cwltool.builder.Builder attribute) (cwltool.process.Process attribute) formatTime() (cwltool.main.ProvLogFormatter method) fs_access (cwltool.builder.Builder attribute) fsaccess (cwltool.cwlprov.provenance_profile.ProvenanceProfile attribute) (cwltool.cwlprov.ro.ResearchObject attribute) FSAction (class in cwltool.argparser) FSAppendAction (class in cwltool.argparser) full_name (cwltool.cwlprov.provenance_profile.ProvenanceProfile attribute) (cwltool.cwlprov.ro.ResearchObject attribute)

G

ga4gh_tool_registries (in module cwltool.resolver) GA4GH_TRS_FILES (in module cwltool.resolver) GA4GH_TRS_PRIMARY_DESCRIPTOR (in module cwltool.resolver) gather() (in module cwltool.cwlrdf) generate_arg() (cwltool.builder.Builder method) generate_example_input() (in module cwltool.main) generate_input_template() (in module cwltool.main) generate_output_prov() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) generate_parser() (in module cwltool.argparser) generate_prov_doc() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) generate_snapshot() (cwltool.cwlprov.ro.ResearchObject method) generatefiles (cwltool.job.JobBase attribute) generatemapper (cwltool.job.JobBase attribute) generations (cwltool.mutation.MutationManager attribute) get_container_from_software_requirements() (in module cwltool.software_requirements) get_default_args() (in module cwltool.argparser) get_dependencies() (in module cwltool.software_requirements) get_dependency_tree() (in module cwltool.checker) get_dot_graph() (cwltool.cwlviewer.CWLViewer method) get_expressions() (in module cwltool.validate_js)

get_from_requirements() (cwltool.docker.DockerCommandLineJob method) (cwltool.job.ContainerCommandLineJob method) (cwltool.singularity.SingularityCommandLineJob method) get_image() (cwltool.docker.DockerCommandLineJob method) (cwltool.singularity.SingularityCommandLineJob static method) get_listing() (in module cwltool.utils) get_outdir() (cwltool.context.RuntimeContext method) get_overrides() (in module cwltool.process) get_process() (in module cwltool.subgraph) get_requirement() (cwltool.utils.HasReqsHints method) get_schema() (in module cwltool.process) get_stagedir() (cwltool.context.RuntimeContext method) get_step() (in module cwltool.subgraph) get_step_id() (in module cwltool.checker) get_subgraph() (in module cwltool.subgraph) get_tmpdir() (cwltool.context.RuntimeContext method) get_version() (in module cwltool.singularity) getdefault() (in module cwltool.context) glob() (cwltool.stdfsaccess.StdFsAccess method) globals (cwltool.validate_js.JSHintJSReturn attribute)

H

handle_software_environment() (in module cwltool.run_job) has_data_file() (cwltool.cwlprov.ro.ResearchObject method) has_manifest (cwltool.cwlprov.ro.ResearchObject attribute) has_secret() (cwltool.secrets.SecretStore method) Hasher (in module cwltool.cwlprov.provenance_constants) hashes (cwltool.cwlprov.writablebagfile.WritableBagFile attribute) HasReqsHints (class in cwltool.utils) hints (cwltool.builder.Builder attribute) (cwltool.command_line_tool.ExpressionJob attribute) (cwltool.context.LoadingContext attribute) (cwltool.job.JobBase attribute) (cwltool.process.Process attribute) (cwltool.utils.HasReqsHints attribute)

host_provenance (cwltool.context.LoadingContext attribute) (cwltool.cwlprov.provenance_profile.ProvenanceProfile attribute) host_provenance() (cwltool.cwlprov.ro.ResearchObject method)

I

id (cwltool.workflow_job.WorkflowJobStep attribute) identity() (in module cwltool.update) image_base_path (cwltool.context.RuntimeContext attribute) import_embed() (in module cwltool.pack) in_flight (cwltool.task_queue.TaskQueue attribute) inherit_reqshints() (in module cwltool.main) init_job_order() (in module cwltool.main) initialize_provenance() (cwltool.cwlprov.ro.ResearchObject method) inplace_update (cwltool.job.JobBase attribute) INPUT (in module cwltool.subgraph) INPUT_OBJ_VOCAB (in module cwltool.builder) inputs_object cwltool command line option inputs_record_schema (cwltool.process.Process attribute) INTERNAL_VERSION (in module cwltool.update) is_all_output_method_loop_step() (in module cwltool.checker)

is_apptainer_1_1_or_newer() (in module cwltool.singularity) is_apptainer_1_or_newer() (in module cwltool.singularity) is_conditional_step() (in module cwltool.checker) is_expression() (in module cwltool.validate_js) is_version_2_6() (in module cwltool.singularity) is_version_3_10_or_newer() (in module cwltool.singularity) is_version_3_1_or_newer() (in module cwltool.singularity) is_version_3_4_or_newer() (in module cwltool.singularity) is_version_3_9_or_newer() (in module cwltool.singularity) is_version_3_or_newer() (in module cwltool.singularity) isdir() (cwltool.stdfsaccess.StdFsAccess method) isfile() (cwltool.stdfsaccess.StdFsAccess method) items() (cwltool.pathmapper.PathMapper method) items_exclude_children() (cwltool.pathmapper.PathMapper method) iterable (cwltool.workflow_job.WorkflowJobStep attribute) iteration (cwltool.workflow_job.WorkflowJobLoopStep attribute)

J

job (cwltool.builder.Builder attribute) (cwltool.command_line_tool.CallbackJob attribute) job() (cwltool.command_line_tool.AbstractOperation method) (cwltool.command_line_tool.CommandLineTool method) (cwltool.command_line_tool.ExpressionTool method) (cwltool.process.Process method) (cwltool.procgenerator.ProcessGenerator method) (cwltool.procgenerator.ProcessGeneratorJob method) (cwltool.workflow.Workflow method) (cwltool.workflow.WorkflowStep method) (cwltool.workflow_job.WorkflowJob method) (cwltool.workflow_job.WorkflowJobLoopStep method) (cwltool.workflow_job.WorkflowJobStep method) job_script_provider (cwltool.builder.Builder attribute) (cwltool.context.RuntimeContext attribute) JobBase (class in cwltool.job)

jobdefaults (cwltool.context.LoadingContext attribute) JobExecutor (class in cwltool.executors) jobloader_id_name (in module cwltool.load_tool) jobloaderctx (in module cwltool.load_tool) joborder (cwltool.job.JobBase attribute) (cwltool.workflow_job.WorkflowJobLoopStep attribute) jobout (cwltool.procgenerator.ProcessGeneratorJob attribute) JobsGeneratorType (in module cwltool.utils) JobsType (in module cwltool.utils) join() (cwltool.stdfsaccess.StdFsAccess method) (cwltool.task_queue.TaskQueue method) js_console (cwltool.builder.Builder attribute) (cwltool.context.RuntimeContext attribute) js_hint_options_file (cwltool.context.LoadingContext attribute) jshint_js() (in module cwltool.validate_js) JSHintJSReturn (class in cwltool.validate_js) JSONType (in module cwltool.utils)

L

lastpart() (in module cwltool.cwlrdf) listdir() (cwltool.stdfsaccess.StdFsAccess method) load() (cwltool.mpi.MpiConfig class method) load_job_order() (in module cwltool.main) load_overrides() (in module cwltool.load_tool) load_tool() (in module cwltool.load_tool) loader (cwltool.context.LoadingContext attribute) loading_context (cwltool.factory.Factory attribute) LoadingContext (class in cwltool.context) loadingContext (cwltool.procgenerator.ProcessGenerator attribute) loadListing (cwltool.builder.Builder attribute)

LoadListingType (in module cwltool.utils) LoadRefType (in module cwltool.pack) local_path() (in module cwltool.utils) lock (cwltool.task_queue.TaskQueue attribute) log_dir (cwltool.context.RuntimeContext attribute) log_dir_handler (cwltool.context.RuntimeContext attribute) log_handler() (in module cwltool.context) LogAsDebugFilter (class in cwltool.process) LOGS (in module cwltool.cwlprov.provenance_constants) loop_callback() (cwltool.workflow_job.WorkflowJobLoopStep method) loop_checker() (in module cwltool.checker)

M

made_progress (cwltool.workflow_job.WorkflowJob attribute) MAIN (in module cwltool.cwlprov.provenance_constants) main() (in module cwltool.env_to_stdout) (in module cwltool.main) (in module cwltool.run_job) make() (cwltool.factory.Factory method) make_fs_access (cwltool.builder.Builder attribute) (cwltool.context.RuntimeContext attribute) make_job_runner() (cwltool.command_line_tool.CommandLineTool method) make_path_mapper (cwltool.job.JobBase attribute) make_path_mapper() (cwltool.command_line_tool.CommandLineTool static method) make_relative() (in module cwltool.main) make_template() (in module cwltool.main) make_tool() (in module cwltool.load_tool) make_tool_notimpl() (in module cwltool.context) make_workflow_step() (cwltool.workflow.Workflow method) mapper() (cwltool.pathmapper.PathMapper method) MapperEnt (class in cwltool.pathmapper) match_types() (in module cwltool.workflow_job) max_cores (cwltool.executors.MultithreadedJobExecutor attribute) max_cuda (cwltool.executors.MultithreadedJobExecutor attribute) max_ram (cwltool.executors.MultithreadedJobExecutor attribute) mediatype (cwltool.cwlprov.Aggregate attribute) merge_flatten_type() (in module cwltool.checker) mergedirs() (in module cwltool.process) metadata (cwltool.context.LoadingContext attribute) (cwltool.process.Process attribute) METADATA (in module cwltool.cwlprov.provenance_constants) missing_subset() (in module cwltool.checker) module cwltool cwltool.__main__ cwltool.argparser cwltool.builder cwltool.checker cwltool.command_line_tool cwltool.context cwltool.cuda cwltool.cwlprov cwltool.cwlprov.provenance_constants cwltool.cwlprov.provenance_profile cwltool.cwlprov.ro cwltool.cwlprov.writablebagfile cwltool.cwlrdf cwltool.cwlviewer cwltool.docker cwltool.docker_id cwltool.env_to_stdout cwltool.errors cwltool.executors cwltool.factory cwltool.flatten cwltool.job cwltool.load_tool cwltool.loghandler cwltool.main cwltool.mpi cwltool.mutation cwltool.pack cwltool.pathmapper cwltool.process cwltool.procgenerator cwltool.resolver cwltool.run_job cwltool.secrets cwltool.singularity cwltool.singularity_utils cwltool.software_requirements cwltool.stdfsaccess cwltool.subgraph cwltool.task_queue cwltool.udocker cwltool.update cwltool.utils cwltool.validate_js cwltool.workflow cwltool.workflow_job

move_outputs (cwltool.context.RuntimeContext attribute) mpi_config (cwltool.context.RuntimeContext attribute) mpi_procs (cwltool.job.JobBase attribute) MpiConfig (class in cwltool.mpi) MpiConfigT (in module cwltool.mpi) MPIRequirementName (in module cwltool.mpi) msg (cwltool.command_line_tool.ParameterOutputWorkflowException attribute) MultithreadedJobExecutor (class in cwltool.executors) mutation_manager (cwltool.builder.Builder attribute) (cwltool.context.RuntimeContext attribute) MutationManager (class in cwltool.mutation)

N

name (cwltool.context.RuntimeContext attribute) (cwltool.cwlprov.AuthoredBy attribute) (cwltool.job.JobBase attribute) (cwltool.workflow_job.WorkflowJob attribute) (cwltool.workflow_job.WorkflowJobStep attribute) names (cwltool.builder.Builder attribute) (cwltool.process.Process attribute) needs_shell_quoting_re (in module cwltool.job)

nestdir() (in module cwltool.process) nested_crossproduct_scatter() (in module cwltool.workflow_job) networkaccess (cwltool.job.JobBase attribute) neverquote() (in module cwltool.job) no_match_user (cwltool.context.RuntimeContext attribute) no_read_only (cwltool.context.RuntimeContext attribute) NoopJobExecutor (class in cwltool.executors) normalizeFilesDirs() (in module cwltool.utils) nproc_flag (cwltool.mpi.MpiConfig attribute)

O

objclass (cwltool.argparser.DirectoryAction attribute) (cwltool.argparser.DirectoryAppendAction attribute) (cwltool.argparser.FileAction attribute) (cwltool.argparser.FileAppendAction attribute) (cwltool.argparser.FSAction attribute) (cwltool.argparser.FSAppendAction attribute) object_from_state() (in module cwltool.workflow_job) on_error (cwltool.context.RuntimeContext attribute) open() (cwltool.stdfsaccess.StdFsAccess method) open_log_file_for_activity() (in module cwltool.cwlprov.writablebagfile) orcid (cwltool.context.LoadingContext attribute) (cwltool.context.RuntimeContext attribute) (cwltool.cwlprov.AuthoredBy attribute) (cwltool.cwlprov.provenance_profile.ProvenanceProfile attribute) (cwltool.cwlprov.ro.ResearchObject attribute) ORCID (in module cwltool.cwlprov.provenance_constants) ORDERED_VERSIONS (in module cwltool.update) ORE (in module cwltool.cwlprov.provenance_constants) ORIGINAL_CWLVERSION (in module cwltool.update) original_hints (cwltool.process.Process attribute)

original_requirements (cwltool.process.Process attribute) out (cwltool.factory.WorkflowStatus attribute) outdir (cwltool.builder.Builder attribute) (cwltool.command_line_tool.CallbackJob attribute) (cwltool.command_line_tool.ExpressionJob attribute) (cwltool.context.RuntimeContext attribute) (cwltool.job.JobBase attribute) (cwltool.workflow_job.WorkflowJob attribute) OUTPUT (in module cwltool.subgraph) output_buffer (cwltool.workflow_job.WorkflowJobLoopStep attribute) output_callback (cwltool.command_line_tool.CallbackJob attribute) (cwltool.command_line_tool.ExpressionJob attribute) (cwltool.job.JobBase attribute) (cwltool.workflow_job.ReceiveScatterOutput attribute) output_callback() (cwltool.executors.JobExecutor method) output_dirs (cwltool.executors.JobExecutor attribute) OutputCallbackType (in module cwltool.utils) OutputPortsType (in module cwltool.command_line_tool) outputs_record_schema (cwltool.process.Process attribute) overrides_ctx (in module cwltool.load_tool) overrides_list (cwltool.context.LoadingContext attribute)

P

pack() (in module cwltool.pack) packed_workflow() (in module cwltool.cwlprov.writablebagfile) parallel_steps() (in module cwltool.workflow_job) parameter (cwltool.utils.WorkflowStateItem attribute) ParameterOutputWorkflowException ParametersType (in module cwltool.utils) parent (cwltool.process.LogAsDebugFilter attribute) part_of (cwltool.context.RuntimeContext attribute) pass_through_env_vars() (cwltool.mpi.MpiConfig method) path_check_mode (cwltool.command_line_tool.CommandLineTool attribute) path_mapper (cwltool.context.RuntimeContext attribute) PathCheckingMode (class in cwltool.command_line_tool) PathMapper (class in cwltool.pathmapper) pathmapper (cwltool.builder.Builder attribute) (cwltool.job.JobBase attribute) pending_jobs (cwltool.executors.MultithreadedJobExecutor attribute) pending_jobs_lock (cwltool.executors.MultithreadedJobExecutor attribute) permanentFailCodes (cwltool.job.JobBase attribute) podman (cwltool.context.LoadingContext attribute) (cwltool.context.RuntimeContext attribute) PodmanCommandLineJob (class in cwltool.docker) port (cwltool.command_line_tool.ParameterOutputWorkflowException attribute) posix_path() (in module cwltool.utils) postScatterEval (cwltool.context.RuntimeContext attribute) prepare_environment() (cwltool.job.JobBase method) preserve_entire_environment (cwltool.context.RuntimeContext attribute)

preserve_environment (cwltool.context.RuntimeContext attribute) print_js_hint_messages() (in module cwltool.validate_js) print_pack() (in module cwltool.main) print_targets() (in module cwltool.main) printdeps() (in module cwltool.main) printdot() (in module cwltool.cwlrdf) printrdf() (in module cwltool.cwlrdf) Process (class in cwltool.process) process_monitor() (cwltool.job.JobBase method) process_run_id (cwltool.context.RuntimeContext attribute) processDFS() (in module cwltool.checker) processes_to_kill (in module cwltool.utils) ProcessGenerator (class in cwltool.procgenerator) ProcessGeneratorJob (class in cwltool.procgenerator) processStatus (cwltool.procgenerator.ProcessGeneratorJob attribute) (cwltool.workflow_job.ReceiveScatterOutput attribute) (cwltool.workflow_job.WorkflowJob attribute) (cwltool.workflow_job.WorkflowJobLoopStep attribute) procgenerator (cwltool.procgenerator.ProcessGeneratorJob attribute) prospective_prov() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) prov_deps() (in module cwltool.main) prov_host (cwltool.context.RuntimeContext attribute) prov_user (cwltool.context.RuntimeContext attribute) PROVENANCE (in module cwltool.cwlprov.provenance_constants) ProvenanceProfile (class in cwltool.cwlprov.provenance_profile) ProvLogFormatter (class in cwltool.main) pull_image (cwltool.context.RuntimeContext attribute)

Q

quote_id_if_necessary (in module cwltool.cwlviewer)

R

random_outdir() (in module cwltool.utils) readable() (cwltool.cwlprov.writablebagfile.WritableBagFile method) realize_input_schema() (in module cwltool.main) realpath() (cwltool.stdfsaccess.StdFsAccess method) receive_output() (cwltool.procgenerator.ProcessGeneratorJob method) (cwltool.workflow.WorkflowStep method) (cwltool.workflow_job.WorkflowJob method) receive_scatter_output() (cwltool.workflow_job.ReceiveScatterOutput method) ReceiveScatterOutput (class in cwltool.workflow_job) record_process_end() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) record_process_start() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) recursive_resolve_and_validate_document() (in module cwltool.load_tool) register_mutation() (cwltool.mutation.MutationManager method) register_reader() (cwltool.mutation.MutationManager method) rel_path (cwltool.cwlprov.writablebagfile.WritableBagFile attribute) relativised_input_object (cwltool.cwlprov.ro.ResearchObject attribute) relax_path_checks (cwltool.context.LoadingContext attribute) RELAXED (cwltool.command_line_tool.PathCheckingMode attribute) release_reader() (cwltool.mutation.MutationManager method) relink_initialworkdir() (in module cwltool.job) relocateOutputs() (in module cwltool.process) remove_path() (in module cwltool.command_line_tool) replace_refs() (in module cwltool.pack) requirements (cwltool.builder.Builder attribute) (cwltool.command_line_tool.ExpressionJob attribute) (cwltool.context.LoadingContext attribute) (cwltool.job.JobBase attribute) (cwltool.process.Process attribute) (cwltool.utils.HasReqsHints attribute) research_object (cwltool.cwlprov.provenance_profile.ProvenanceProfile attribute) (cwltool.cwlprov.writablebagfile.WritableBagFile attribute) ResearchObject (class in cwltool.cwlprov.ro) resolve_and_validate_document() (in module cwltool.load_tool)

resolve_ga4gh_tool() (in module cwltool.resolver) resolve_host() (cwltool.cwlprov.ro.ResearchObject method) resolve_local() (in module cwltool.resolver) resolve_overrides() (in module cwltool.load_tool) resolve_tool_uri() (in module cwltool.load_tool) resolve_user() (cwltool.cwlprov.ro.ResearchObject method) resolved (cwltool.pathmapper.MapperEnt attribute) resolver (cwltool.context.LoadingContext attribute) ResolverType (in module cwltool.utils) resources (cwltool.builder.Builder attribute) result() (cwltool.procgenerator.ProcessGenerator method) retrieve() (cwltool.secrets.SecretStore method) reversemap() (cwltool.pathmapper.PathMapper method) revmap_file() (in module cwltool.command_line_tool) rm_container (cwltool.context.RuntimeContext attribute) rm_tmpdir (cwltool.context.RuntimeContext attribute) RO (in module cwltool.cwlprov.provenance_constants) ro_uuid (cwltool.cwlprov.ro.ResearchObject attribute) run() (cwltool.command_line_tool.CallbackJob method) (cwltool.command_line_tool.ExpressionJob method) (cwltool.job.CommandLineJob method) (cwltool.job.ContainerCommandLineJob method) (cwltool.job.JobBase method) (cwltool.workflow_job.WorkflowJob method) (in module cwltool.main) run_job() (cwltool.executors.MultithreadedJobExecutor method) run_jobs() (cwltool.executors.JobExecutor method) (cwltool.executors.MultithreadedJobExecutor method) (cwltool.executors.NoopJobExecutor method) (cwltool.executors.SingleJobExecutor method) runner (cwltool.mpi.MpiConfig attribute) runtime_context (cwltool.factory.Factory attribute) RuntimeContext (class in cwltool.context)

S

salad_files (in module cwltool.process) scandeps() (in module cwltool.process) ScatterDestinationsType (in module cwltool.utils) ScatterOutputCallbackType (in module cwltool.utils) SCHEMA (in module cwltool.cwlprov.provenance_constants) SCHEMA_ANY (in module cwltool.process) SCHEMA_CACHE (in module cwltool.process) SCHEMA_DIR (in module cwltool.process) SCHEMA_FILE (in module cwltool.process) schemaDefs (cwltool.builder.Builder attribute) (cwltool.process.Process attribute) script (cwltool.command_line_tool.ExpressionJob attribute) secret_store (cwltool.context.RuntimeContext attribute) secrets (cwltool.secrets.SecretStore attribute) SecretStore (class in cwltool.secrets) seekable() (cwltool.cwlprov.writablebagfile.WritableBagFile method) select_resources (cwltool.context.RuntimeContext attribute) select_resources() (cwltool.executors.MultithreadedJobExecutor method) self_check() (cwltool.cwlprov.ro.ResearchObject method) separateDirs (cwltool.pathmapper.PathMapper attribute) set_env_vars() (cwltool.mpi.MpiConfig method) set_generation() (cwltool.mutation.MutationManager method) set_log_dir (cwltool.context.RuntimeContext attribute) set_log_dir() (in module cwltool.context) setTotal() (cwltool.workflow_job.ReceiveScatterOutput method) setup() (cwltool.pathmapper.PathMapper method) setup_loadingContext() (in module cwltool.main) setup_schema() (in module cwltool.main) SHA1 (in module cwltool.cwlprov.provenance_constants) SHA256 (in module cwltool.cwlprov.provenance_constants) SHA512 (in module cwltool.cwlprov.provenance_constants) shared_file_lock() (in module cwltool.utils) SHELL_COMMAND_TEMPLATE (in module cwltool.job) shortname() (in module cwltool.process) SingleJobExecutor (class in cwltool.executors) singularity (cwltool.context.LoadingContext attribute) (cwltool.context.RuntimeContext attribute) singularity_supports_userns() (in module cwltool.singularity_utils) SingularityCommandLineJob (class in cwltool.singularity)

size() (cwltool.stdfsaccess.StdFsAccess method) skip_resolve_all (cwltool.context.LoadingContext attribute) skip_schemas (cwltool.context.LoadingContext attribute) SNAPSHOT (in module cwltool.cwlprov.provenance_constants) SOFTWARE_REQUIREMENTS_ENABLED (in module cwltool.software_requirements) stage_files() (in module cwltool.process) staged (cwltool.pathmapper.MapperEnt attribute) stagedir (cwltool.builder.Builder attribute) (cwltool.context.RuntimeContext attribute) (cwltool.job.JobBase attribute) (cwltool.pathmapper.PathMapper attribute) start_process() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) state (cwltool.workflow_job.WorkflowJob attribute) static_checker() (in module cwltool.checker) status (cwltool.factory.WorkflowStatus attribute) stderr (cwltool.job.JobBase attribute) StdFsAccess (class in cwltool.stdfsaccess) stdin (cwltool.job.JobBase attribute) stdout (cwltool.job.JobBase attribute) step (cwltool.workflow_job.WorkflowJobLoopStep attribute) (cwltool.workflow_job.WorkflowJobStep attribute) STEP (in module cwltool.subgraph) steps (cwltool.workflow.Workflow attribute) (cwltool.workflow_job.ReceiveScatterOutput attribute) (cwltool.workflow_job.WorkflowJob attribute) StepType (in module cwltool.utils) store() (cwltool.secrets.SecretStore method) streaming_allowed (cwltool.context.RuntimeContext attribute) STRICT (cwltool.command_line_tool.PathCheckingMode attribute) strict (cwltool.context.LoadingContext attribute) strict_cpu_limit (cwltool.context.RuntimeContext attribute) strict_memory_limit (cwltool.context.RuntimeContext attribute) submitted (cwltool.workflow_job.WorkflowJobStep attribute) substitute() (in module cwltool.builder) success (cwltool.utils.WorkflowStateItem attribute) successCodes (cwltool.job.JobBase attribute) supported_cwl_versions() (in module cwltool.main) supportedProcessRequirements (in module cwltool.process) SuppressLog (class in cwltool.validate_js)

T

t (cwltool.factory.Callable attribute) tagfiles (cwltool.cwlprov.ro.ResearchObject attribute) target (cwltool.pathmapper.MapperEnt attribute) task_queue (cwltool.task_queue.TaskQueue attribute) task_queue_threads (cwltool.task_queue.TaskQueue attribute) TaskQueue (class in cwltool.task_queue) temp_prefix (cwltool.cwlprov.ro.ResearchObject attribute) temporaryFailCodes (cwltool.job.JobBase attribute) TEXT_PLAIN (in module cwltool.cwlprov.provenance_constants) thread_count (cwltool.task_queue.TaskQueue attribute) timelimit (cwltool.job.JobBase attribute) timeout (cwltool.builder.Builder attribute) tmp_outdir_prefix (cwltool.context.RuntimeContext attribute) tmpdir (cwltool.builder.Builder attribute) (cwltool.command_line_tool.ExpressionJob attribute) (cwltool.context.RuntimeContext attribute) (cwltool.job.JobBase attribute)

TMPDIR_LOCK (in module cwltool.executors) tmpdir_prefix (cwltool.context.RuntimeContext attribute) tool (cwltool.process.Process attribute) (cwltool.workflow_job.WorkflowJob attribute) (cwltool.workflow_job.WorkflowJobStep attribute) tool_dependency_dir (cwltool.software_requirements.DependenciesConfiguration attribute) tool_resolver() (in module cwltool.resolver) toplevel (cwltool.context.RuntimeContext attribute) tostr() (cwltool.builder.Builder method) total (cwltool.workflow_job.ReceiveScatterOutput attribute) trim_listing() (in module cwltool.utils) truncate() (cwltool.cwlprov.writablebagfile.WritableBagFile method) try_make_job() (cwltool.workflow_job.WorkflowJob method) type (cwltool.pathmapper.MapperEnt attribute)

U

UDockerCommandLineJob (class in cwltool.udocker) uniquename() (in module cwltool.process) unset_generation() (cwltool.mutation.MutationManager method) UnsupportedRequirement UP (in module cwltool.subgraph) update() (cwltool.pathmapper.PathMapper method) (in module cwltool.update) update_index() (in module cwltool.load_tool) updatePathmap() (cwltool.command_line_tool.CommandLineTool method) UPDATES (in module cwltool.update) upgrade_lock() (in module cwltool.utils) uri (cwltool.cwlprov.Aggregate attribute) (cwltool.cwlprov.AuthoredBy attribute)

urljoin (cwltool.argparser.FSAction attribute) (cwltool.argparser.FSAppendAction attribute) use_container (cwltool.context.RuntimeContext attribute) use_custom_schema() (in module cwltool.process) use_standard_schema() (in module cwltool.process) used_artefacts() (cwltool.cwlprov.provenance_profile.ProvenanceProfile method) used_by_step() (in module cwltool.workflow) user_provenance (cwltool.context.LoadingContext attribute) (cwltool.cwlprov.provenance_profile.ProvenanceProfile attribute) user_provenance() (cwltool.cwlprov.ro.ResearchObject method) user_space_docker_cmd (cwltool.context.RuntimeContext attribute) USER_UUID (in module cwltool.cwlprov.provenance_constants) UUID (in module cwltool.cwlprov.provenance_constants)

V

v1_0to1_1() (in module cwltool.update) v1_1_0dev1to1_1() (in module cwltool.update) v1_1to1_2() (in module cwltool.update) v1_2_0dev1todev2() (in module cwltool.update) v1_2_0dev2todev3() (in module cwltool.update) v1_2_0dev3todev4() (in module cwltool.update) v1_2_0dev4todev5() (in module cwltool.update) v1_2_0dev5to1_2() (in module cwltool.update) v1_2to1_3dev1() (in module cwltool.update) validate_hints() (cwltool.process.Process method) validate_js_expressions() (in module cwltool.validate_js)

validate_only (cwltool.context.RuntimeContext attribute) validate_stdout (cwltool.context.RuntimeContext attribute) value (cwltool.utils.WorkflowStateItem attribute) var_spool_cwl_detector() (in module cwltool.process) versionstring() (in module cwltool.utils) visit() (cwltool.pathmapper.PathMapper method) (cwltool.process.Process method) (cwltool.workflow.Workflow method) (cwltool.workflow.WorkflowStep method) visit_class() (in module cwltool.utils) visit_field() (in module cwltool.utils) visitlisting() (cwltool.pathmapper.PathMapper method)

W

wait_for_next_completion() (cwltool.executors.MultithreadedJobExecutor method) WF4EVER (in module cwltool.cwlprov.provenance_constants) WFDESC (in module cwltool.cwlprov.provenance_constants) WFPROV (in module cwltool.cwlprov.provenance_constants) windows_check() (in module cwltool.main) Workflow (class in cwltool.workflow) workflow (cwltool.workflow_job.WorkflowJob attribute) WORKFLOW (in module cwltool.cwlprov.provenance_constants) workflow_eval_lock (cwltool.context.RuntimeContext attribute) workflow_job_step_name_callback (cwltool.context.RuntimeContext attribute) workflow_run_uri (cwltool.cwlprov.provenance_profile.ProvenanceProfile attribute)

workflow_run_uuid (cwltool.cwlprov.provenance_profile.ProvenanceProfile attribute) WorkflowJob (class in cwltool.workflow_job) WorkflowJobLoopStep (class in cwltool.workflow_job) WorkflowJobStep (class in cwltool.workflow_job) WorkflowStateItem (class in cwltool.utils) WorkflowStatus WorkflowStep (class in cwltool.workflow) writable (cwltool.utils.DirentType attribute) WritableBagFile (class in cwltool.cwlprov.writablebagfile) write() (cwltool.cwlprov.writablebagfile.WritableBagFile method) write_bag_file() (in module cwltool.cwlprov.writablebagfile)